Microbial decomposition of soil organic matter is a key component of the global carbon cycle. As Earth’s climate changes, the response of microbes and microbial enzymes to rising temperatures will largely determine the soil carbon feedback to atmospheric CO2. While increasing attention focuses on physiological and ecological mechanisms of microbial responses, the role of evolutionary adaptation remains little studied. To address this gap, we developed an ecosystem-evolutionary model of a soil microbe-enzyme system under warming. Constraining the model with observations from five contrasting sites reveals evolutionary aggravation of soil carbon loss to be the most likely outcome; however, temperature-dependent increases in mortality could cause an evolutionary buffering effect instead. We generally predict a strong latitudinal pattern, from small evolutionary effects at low latitude to large evolutionary effects at high latitudes. Accounting for microbial evolutionary adaptation will likely be critical for improving projections of Earth system responses to climate change.